Jaroslav KOCA

Full Professor of Chemistry. MS degree (mathematics and chemistry) from J.E. Purkyne University, Brno, Czech Republic (with dr. Ivan Novotny); PhD degree from Komensky University, Bratislava, Slovakia (with professors Miroslav Simek and Milan Kratochvil); DSc from Masaryk University, Brno; 2 years postdoctoral fellow of Royal Norwegian Council for Scientific and Industrial Research (NTNF, with professor Per H.J. Carlsen).

Visiting professor or researcher: Grenoble (France), Pacific Nortwest National Laboratory, Washington (USA), Rennes (France), Trondheim (Norway), Nantes (France), Knoxville, Tennessee (USA), Athens (Greece).

Faculty member in Undegraduate and Graduate Program in Theoretical and Computer Assisted Chemistry, Education in Chemistry, Computer Modeling and Simulations in Chemistry, Biology and Environmental Science at National Centre for Biomolecular Research (formerly Laboratory of Biomolecular Structure and Dynamics) and Department of  Chemistry, Faculty of Science, Masaryk University , Brno, Czech Republic. Currently serving as a director of  National Centre for Biomolecular Research and Scientific Director of Central European Institute of Technology (CEITEC) .











Computational chemistry and molecular modeling focused on structure and dynamics of biologically interesting flexible molecules (carbohydrates, peptides, oligonucleotides, proteins, biomolecular complexes), development of methodology (program CICADA and others), computer assisted organic synthesis (a general model developed is called "Synthon Model of Organic Chemistry"), computer studies of enzymatic reactions and interactions, computer studies of supramolecules. Current interests include also molecular dynamics on oligonucleotides, proteins, carbohydrates, their complexes, and simulations in mixed solvents. Results published in more than 170 journal and conference papers, and book chapters.



Molecular dynamics is used to study conformational behavior of proteins, nucleic acids fragments and molecular complexes. Novel methodologies like Locally Enhanced Sampling and continuum solvent representations are tested against classical approaches. Number of analysis methods are used to examine resulting trajectories to obtain as much as information from time consuming calculations as possible. Also interactions of solute with solvent molecules are explored. Results are compared with available experimental data (especially NMR and X-ray). Research include, for example:

    Cyclin dependent kinase cdk2:                                     Phosphotriesterase:                                           Oligonucleotides:                 


                                    Glycosytransferases:                                                                            Lectins:



is a package of programs devoted to conformational analysis and molecular docking. It performs description of conformational/configurational space in terms of energy minima (e.g., conformers on conformational Potential Energy hyperSurface) and pathways connecting them (e.g.,  conformational interconversions). The data obtained are used to simulate propagation in conformational movement using Boltzmann statistics (COMBINE software). Resulting trajectories give an information about concerted conformational movement and other interesting phenomena occuring at molecular level.


                    Search for pathways on PES                                                        Cyclodextrine docking





An attempt has been made to evaluate the phenomena which is called molecular flexibility. Flexibility is calculated for single conformers, molecular fragments (like freely rotatable single bonds) as well as entire molecule. It is evaluated in absolute and relative scale.



is a general mathematical model which is based on a complete set of valence states of atoms within the so-called octet chemistry (s,p-chemistry). The model makes it possible to generate all the possible reaction mechanisms within octet chemistry, and all the possible interconversion schemes between any couple of valence states of atoms.



Structure and dynamics of supramolecules are solved by combining theoretical and experimental methods. Properties of experimentally prepared amides and calix[n]arenes and their complexes with anions are studied by molecular modeling. The aim is to design ligands with defined specificity for anions.


SELECTED PAPERS (For fresh update see ORCID ID:  http://orcid.org/0000-0002-2780-4901 )

  1. Mishra S.K., Sund J., Aqvist J., Koca J.: Computational Prediction of Monosaccharide Binding Free Energies to Lectins with Linear Interaction Energy Models.  J.Comput. Chem. 2012, 000, 00–00. DOI: 10.1002/jcc.23081

  2. Kozmon S., Matuska R., Spiwok V,  Koca J.: Three-Dimensional Potential Energy Surface of Selected Carbohydrates’ CH/π Dispersion Interactions Calculated by High-Level Quantum Mechanical Methods. Chemistry - A European Journal 17, 5680–5690 (2011).

  3. Mishra N.K., Kriz Z., Wimmerova M.,  Koca J.: Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations. Carb. Res. 345, 1432-1441 (2010).

  4. Wiesner J., Kriz Z., Kuca K., Jun D., Koca J.: Why acetylcholinesterase reactivators do not work in butyrylcholinesterase. J. Enzyme Inhib. Med. Chem. 25,  318-322  (2010).

  5. Wiesner J., Kriz Z., Kuca K., Jun D., Koca J.: Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics. J. Biomol. Struct. Dyn. 28, 393-403 (2010).

  6. Jirouskova Z., Svobodova Varekova R., Vanek J.,  Koca J.: Electronegativity Equalization Method: Parameterization and Validation for Organic Molecules using the Merz- Kollman-Singh Charge Distribution Scheme. J. Comput. Chem. 30, 1174-1178 (2009).
  7. Wimmerova M, Mishra NK, Pokorna M, Koca J.: Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis. J. Mol. Mod. 15, 673-679  (2009).
  8. Adam J., Kriz Z., Prokop M., Wimmerova M., Koca J.:  In Silico Mutagenesis and Docking Studies of Pseudomonas aeruginosa PA-IIL Lectin s Predicting Binding Modes and Energies.  J. Chem. Inf. Model. 48, 2234-2242 (2008).
  9. Prokop M., Adam J., Kriz Z.,  Wimmerova M., Koca J.:  TRITON: a graphical tool for ligand-binding protein engineering. Bioinformatics 24, 1955-1956 (2008)
  10. Bartova I., Koca J., Otyepka M.: Regulatory Phosphorylations of Cyclin-Dependent Kinase 2: An Insight from the Molecular Dynamics Simulations.  J. Mol. Mod. 14, 761-768 (2008)
  11. Matousek J.,  Cajan M., Kulhanek P., Koca J.: Mechanism of Hydrogen Bond Array Isomerization in Tetrahydroxycalix[4]arene and Tetrahydroxythiacalix[4]arene. J. Phys. Chem. A 112, 1076-1084 (2008)
  12. Otyepka M., Bartova I., Koca J.: Functional Flexibility of Human Cyclin-Dependent Kinase-2 and Its Evolutionarily Conservation. Protein Sci.  17, 22-33 (2008)
  13. Mishra N.K.,  Kulhanek P.,  Snajdrova L.,  Petrek, M., Imberty A., Koca J.: Molecular Dynamics Study of Pseudomonas aeruginosa Lectin-II Complexed with Monosaccharides. Proteins: Structure, Function, and Bioinformatics 72, 382-392 (2008)
  14. Petrek M., Kosinova M., Otyepka M., Koca J.: MOLE: An Explorer of Molecular Channels, Pores and Tunnels on the Voronoi Meshes. Structure 15, 1357-1363 (2007)
  15. Reblova K., Fadrna E., Sarzynska J., Kulinski T., Kulhanek P., Ennifar E., Koca J., Sponer J.: Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by Molecular Dynamics. Biophys. J. 93, 3932-3949 (2007)
  16. Wiesner J., Kriz Z., Kuca K., Jun D., Koca J.: Acetylcholinesterases – the structural similarities and differences. Journal of Enzyme Inhibition and Medicinal Chemistry 22, 417-424 (2007)
  17. Razga F., Koca J., Mokdad A., Sponer J., Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Research, 35, 4007-4017 (2007)
  18. Svobodova Varekova R.,  Jirouskova Z., Vanek J., Suchomel S., Koca J.: Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule. Int. J. Mol. Sci. 8, 572-582 (2007)

19.  Otyepka M., Bartova I., Kriz Z., Koca J.: Different Mechanisms of CDK5 and CDK2 Activation as Revealed by CDK5/P25 and CDK2/CYCLIN A Dynamics . J. Biol. Chem. 281, 7271-7281 (2006)

20.  Matousek J., Kulhanek P.,  Cajan M., Koca J.: The Effect of Solvation on Pinched Cone - Pinched Cone Interconversion of Tetraethoxycalix[4]arene and Tetraethoxythiacalix[4]arene. J. Phys. Chem. A 110, 861-867 (2006)


21.  Imberty A., Wimmerova M., Koca J., Breton C.: Molecular modelling of glycosyltransferases.  In Glycobiology Protocols (Brokhausen-Schutzbach, I., ed.), Series “'Methods in Molecular Biology”, The Humana Press Inc., Totowa NJ,  145-156 (2006).

22.  Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J., Damborsky, J.: CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities. BMC Bioinformatics 7, 316-324 (2006)

  1. Reblova K.,  Lankas F., Razga F., Krasovska M.,  Koca J.,  Sponer J.: Structure, dynamics and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers 82,  504-520 (2006).

24.  Svobodova-Varekova R., Koca J.: Optimized and Parallelized Implementation of the Electronegativity Equalization Method and the Atom-Bond Electronegativity Equalization Method. J. Comput. Chem 27, 396-405  (2006).

25.  Breton C.,  Snajdrova L.,  Jeanneau C., Koca J.,  Imberty A.: Structures and mechanisms of glycosyltransferases. Glycobiology 16, 29R-37R (2006).

26.  Razga F., Zacharias M.,  Reblova K., Koca J., Sponer J.:  RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics. Structure 14, 825–835 (2006)

27.  Fadrna E, Hladeckova K., Koca J.: Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study. J. Biomol. Struct. Dyn. 23, 151-162 (2005).

28.  Bartova I., Otyepka M., Kriz Z., Koca J.: The Mechanism of Inhibition of the Cyclin Dependent Kinase 2 as Revealed by the Molecular Dynamics Study on the Complex CDK2 with the Peptide Substrate HHASPRK. Protein Sci. 14445-451 (2005).

29.  Razga F., Koca J., Sponer J., Leontis N.B.: Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases. Biophys. J. 88,  3466-3485 (2005).

30.  Mitchell E.P., Sabin C., Snajdrova L., Pokorna M., Perret S., Gautier C., Hofr C., Gilboa-Garber N., Koca J., Wimmerova M., Imberty A.: High affinity fucose binding of Pseudomonas aeruginosa lectin PA-IIL: 1.0 Å resolution crystal structure of the complex combined with thermodynamics and computational chemistry approaches. Proteins: Structure, Function, and Bioinformatics 58, 735-746 (2005).

31.  Bartova I., Otyepka M., Kriz Z., Koca J.: Activation and Inhibition of Cyclin-Dependent Kinase-2 by Phosphorylation; A Molecular Dynamics Study Reveals the Functional Importance of the Glycine-Rich Loop. Protein Sci. 13, 1449-1457 (2004).

32.  Reblova K., Spackova N., Koca J., Leontis N.B., Sponer J.: Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex.  Biophys. J. 87, 3397-3412 (2004)

33.  Kriz Z., Otyepka M., Bartova I., Koca J.: Analysis of CDK2 Active Site Hydration: A Method to Design New Inhibitors . Proteins: Structure,function,genetics 55, 258-274 (2004).

34.  Razga F, Spackova N, Reblova K, Koca J, Leontis NB, Sponer J.: Ribosomal RNA kink-turn motif - A flexible molecular hinge. J. Biomol. Struct. Dyn.  22, 183-193 (2004).

35.  Kulhanek P., Potacek M., Koca J.: Quantum-Chemical Insight into Mechanism of Combined Intra-Intermolecular Cycloaddition. Coll. Czech. Chem. Commun. 69, 231-241 (2004)

36.  Fadrna E, Spackova N, Stefl R, Koca J, Cheatham TE, Sponer J.: Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations. Biophys J. 87, 227-242  (2004)

37.  Navratilova H., Opatrilová R., Kriz Z., Koca J.: Enantioselective chromatography and molecular modelling of novel aryloxyaminopropanols with alkyl carbamate function. Chirality 16, 139-146 (2004)

38.  Snajdrova L., Kulhanek P., Imbery A., Koca J.: Molecular Dynamics Simulations of Glycosyltransferase LgtC. Carb. Res. 339, 995-1006  (2004)

39.  Cioci G.,  Rivet A., Koca J., Perez S.: Conformational Analysis of Complex Oligosaccharides: The CICADA Approach to the Uromodulin O-Glycans. Carb. Res. 339,  949-959 (2004)

40.  Kulhanek P., Schlag E.W., Koca J.: A Novel Mechanism of Proton Transfer in Protonated Peptides. J. Am. Chem. Soc. 125, 13678-13679 (2003).

41.  Koca J., Zhan, Ch-G., Rittenhouse R., Ornstein R.: Coordination Number of Zinc Ions in the Phosphotriesterase Active Site by Molecular Dynamics and Quantum Mechanics. J. Comput. Chem. 24, 368-378 (2003).

42.  Kulhanek P., Schlag E.W., Koca J.: Mechanism of Proton Transfer in Short Protonated Oligopeptides. I. N-methylacetamide and N2-acetyl-N1-methylglycinamide. J. Phys. Chem. A 107, 5789-5797 (2003)

  1. Reblova K., N. Spackova N., Sponer J.E., Koca J., Sponer J.: Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets . Nucleic Acid Research 31, 6942-6952 (2003).

44.  Reblova K., Spackova N., Stefl R., Csaszar K. Koca J., Leontis N.B., Sponer J.: Non-Watson-Crick basepairing and hydration in RNA motifs: Molecular dynamics of 5S rRNA loop E. Biophys. J. 84, 3564-3582 (2003).

45.  Vrbka L, Klan P., Kriz Z., Koca J., Wagner P.J.:  Computer Modeling and Simulations on Flexible Bifunctional Systems: Intramolecular Energy Transfer Implications. J. Phys. Chem. A 107, 3404-3413 (2003).

46.  Kriz Z., Koca J., Imberty A., Charlot A., Auzély-Velty R.: Investigation of the complexation of (+)-catechin by beta-cyclodextrin by a combination of NMR, microcalorimetry and molecular modeling techniques. Org. Biomol. Chem. 1, 2590-2595 (2003).

  1. Stefl R., Cheatham III T.E., Spackova N., Fadrna E., Berger I., Koca J., Sponer J.: Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates. Biophys J. 85 1787-1804 (2003)

48.  Fadrna E., Koca J.: Conformational flexibility of two RNA trimers explored by computational tools and database search. J. Biomol. Struct. Dyn. 20, 715-731 (2003)

49.  Kriz Z, Koca, J., Carlsen P.: A Computer Program for the Simulation of NOE-Effect in NMR Spectroscopy, and its Implementation into the CICADA Conformational Search Program. Internet Electronic Journal of Molecular Design 2, 55-69 (2003) 

50.  Cajan M., Lhotak P., Lang J., Dvorakova H., Stibor I., Koca J.: The Conformational Behaviour of Thiacalix[4]arenes: The Pinched Cone-Pinched Cone Transition J. Chem. Soc. Perkin. Trans. II  11, 1922-1929 (2002).

51.  Otyepka M., Kriz Z., Koca J.: Binding Modes of Free cdk2 and Its Two Complexes with Inhibitors Studied by Computer Simulations J. Biomol. Struct. Dyn. 20, 141-154 (2002).

52.  Bohac M, Nagata Y, Prokop Z, Prokop M, Monincova M, Tsuda M, Koca J, Damborsky J.: Halide-stabilizing residues of haloalkane dehalogenases studied by quantum mechanic calculations and site-directed mutagenesis. Biochemistry 41, 14272-80 (2002).

53.  Petrova P., Koca J., Imberty : Molecular dynamics simulations of solvated UDP-glucose in interaction with Mg cations. European Journal of Biochemistry  268,  5365-5374 (2001).

54.  Koca J., Zhan Ch-G., Rittenhouse R.C., Ornstein R.: Mobility of the Active Site bound Paraoxon and Sarin in Zinc-Phosphotriesterase by Molecular Dynamics Simulation and Quantum Chemical Calculation. J. Am. Chem. Soc. 123, 817-826 (2001).

55.  Stefl, R., Trantirek, L., Vorlickova, M., Koca, J., Sklenar, V. & Kypr, J.: A-like Guanine-Guanine stacking in aqueous DNA duplex of d(GGGGCCCC). J.Mol. Biol. 307, 513-524 (2001).

56.  Damborsky J., Prokop M., Koca J.: TRITON: graphic software for rational engineering of enzymes. TIBS 26, 71-73 (2001).

57.  Petrova P., Monterio C., Herve du Penhoat C., Koca J., Imberty A.: Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridine diphosphate-glucose in the presence of monovalent cations Biopolymers 58, 617-635 (2001)

58.  Kriz Z., Carlsen P.H.J., Koca J.: Conformational Features of Linear and Cyclic Enkephalins. A Computational Study. Theochem 540 , 231-251 (2001).

59.  Stefl R., Spackova N., Berger I., Koca J., Sponer J.: Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophys. J. 80, 455-468 (2000).

60.  Stefl R., Koca J.: Unrestrained Molecular Dynamics Simulations of d(AT5]2 Duplex in Aqueous Solution: Hydration and Sodium Ions Binding in the Minor Groove. J. Am. Chem. Soc. 122, 5025-5033 (2000).

61.  Prokop M., Damborsky J., Koca J.: TRITON: graphical software for in silico construction of protein mutants and predictions of their activities. Bioinformatics. 16, 845-846 (2000).

62.  Koca J., Ludin M., Perez S., Imberty A.: Single-Coordinate-Driving Method in Molecular Docking. J. Mol. Graphics and Modeling. 18 , 108-118 (2000).

63.  Otyepka M., Krystof V., Havlicek L., Siglerova V., Strnad M., Koca J.: Docking-Based Development of Purine-like Inhibitors of Cdk2. J. Med. Chem. 43 , 2506-2513 (2000).

64.  Petrova P., Koca J., Imberty A.: Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-glucose. Mol. Simul. 24 , 325-340 (2000).

65.  Cajan M., Damborsky J., Stibor I., Koca J.: Quantitative Structure-Property Relationships on the Stability of [Amide]Br- Complexes. J. Chem. Inf. Comp. Sci. 40, 1151-1157 (2000).

66.  Picard C., Gruza J., Derouet C., Renard C., Mazeau K., Koca J., Imberty A. and Herve du Penhoat C.: A conformational study of the xyloglucan oligomer, XXXG, by NMR spectroscopy and molecular modeling. Biopolymers 54 , 11-26 (2000).

67.  Trantirek L., Stefl R., Vorlickova M., Sklenar V., Koca J., Kypr J.: An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings. J. Mol. Biol. 297 , 907-922 (2000).

68.  Petrova P., Koca J., Imberty A.: Potential Energy Surfaces of Nucleotide-Sugars. Ab-Initio Calculations, Force-Field Parametrization and Exploration of the Flexibility. J. Am. Chem. Soc. 121, 5535-5547 (1999).

69.  Stefl R., Fadrna E., Koca J.: Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimers. J. Biomol. Struct. Dyn. 16 , 1087-1095 (1999).

70.  Cajan M., Stibor I., Koca J.: Computational Studies on the Stability of [Amide]Br- Complexes. J. Phys. Chem. 103 , 3778-3782 (1999).

71.  Cernohorsky M., Kettou S., Koca J.: VADER --- New Software for Exploring Interconversions on Potential Energy Surfaces. J. Chem. Inf. Comp. Sci. 39, 705-712 (1999).

72.  Cernohorsky M., Vaultier M., Koca J.: Comparison of Conformational Behavior of the Short Alanine Peptides and Their Boron Analogues. J. Mol. Struct. (Theochem) 489, 213-224 (1999).

73.  Damborsky J., Bohac M., Prokop M., Kuty M, Koca J.: Computational Site-directed Mutagenesis of Haloalkane Dehalogenase in Position 172. Protein. Eng. 11, 901-907 (1998).

74.  Koca J.: Travelling Through Conformational Space - An Approach for Analyzing the Conformational Behaviour of Flexible Molecules. . Progress in Biophys. and Mol. Biol. 70, 137-173 (1998).

75.  Kuty M., Damborsky J., Prokop M., Koca J.: A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 2. Quantum Chemical Study of Complete Reaction Mechanism. J.Chem.Inf.Comp.Sci. 38, 736-741 (1998).

76.  Koca J.: Where Does Computer Chemistry Move - Focused on Larger Molecules Modeling. Chem. Listy 92, 101-113 (1998) (in Czech).

77.  Lynam M.M., Kuty M., Damborsky J., Koca J., Adriaens P.: Molecular Orbital Calculations to Probe Mechanism of Reductive Dechlorination of Polychlorinated Dioxins. Environ. Toxicol. Chem. 17, 988-997 (1998).

78.  Gruza J., Koca J., Perez S., Imberty A.: Comparison of Force-field Parametrizations as Applied to Conformational Analysis of Ribofuranosides. J Mol. Struct (Theochem) 424, 269-280 (1998).

79.  Fadrna E., Koca J.: Single-Coordinate-Driving Method Combined with Simulated Annealing. An Efficient Tool to Search Conformational Space. J.Phys.Chem.B 101, 7863-7868 (1997).

80.  Krooshof G.H., Kwant E.M., Damborsky J., Koca J., Janssen D.B.: Repositioning the Catalytic Triad Aspartic Acid of Haloalkane Dehalogenase: Effect on Stability, Kinetics, and Structure. Biochemistry, 9571-9580 (1997).

81.  Fadrna E., Koca K.: A Combination of Driving Method with Simulated Annealing to Search Conformational Space. J.Mol.Struct. (Theochem) 398-399, 523-528 (1997).

82.  Damborsky J., Kuty M., Nemec M., Koca J.: A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: Quantum Chemical Study of the First Reaction Step. J.Chem.Inf.Comp.Sci. 37, 562-568 (1997).

83.  Fadrna E., Koca J.: CICADA Interface with AMBER. An Application on Oligonucleotides and their Fragments. J.Biomol.Struct.Dynam. 14, 137-152 (1996).

84.  Kriz Z., Koca J., Carlsen P.H.J.: Conformational behavior and flexibility of terminally blocked cysteine and cystine. J.Mol.Mod. 2, 51-61 (1996).

85.  Cernohorsky M., Kuty M., Koca J.: A Multidimensional Driver for Quantum Chemistry Program MOPAC. Comp. & Chem. 32, 35-44 (1996).

86.  Casset F., Imberty A., Herve du Penhoat C., Koca J., Perez S.: Validation of two conformational searching methods applied to sucrose: simulation of NMR and chiro-optical data. J.Mol.Structure (Theochem) 395-396 211-224 (1997).

87.  Koca J.: Computer Simulation of Conformational Movement Based on Interconversion Phenomena. J.Mol.Struct. 343, 125-132 (1995).

88.  Engelsen S., Perez S., Imberty A., Braccini I., Herve du Penhoat C., Koca J.: Travelling on the Potential Energy Surfaces of Carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search. Carbohydrate Research 276, 1-29 (1995).

89.  Koca J., Perez S., Imberty A.: Conformational Analysis and Flexibility of Carbohydrates using the CICADA approach with MM3. J.Comput.Chem. 16, 296-310 (1995).

90.  Matyska L., Koca J.: D-CICADA, a software for conformational PES elucidation on network of workstations. J.Comput.Chem. 15, 937-946 (1994).

91.  Koca J.: Computer program CICADA--travelling along conformational potential energy hypersurface. J.Mol.Struct. (Theochem) 308, 13-24 (1994).

92.  Koca J., Kriz Z., Carlsen P.H.J.: Computer study of conformational flexibility of 20 common amino acids. J.Mol.Struct. 306, 157-164 (1994).

93.  Hladka E., Koca J., Kratochvil M., Kvasnicka V., Matyska L., Pospichal J., Potucek V.: The Synthon Model and Program PEGAS for Computer Assisted Organic Synthesis. Top. Curr. Chem. 166. Springer-Verlag, Berlin, Heidelberg 1993.

94.  Koca J.: Potential Energy Hypersurface and Molecular Flexibility. J.Mol.Struct. 291, 255-269 (1993).

95.  Koca J., Carlsen P.H.J.: Conformational Behavior and Flexibility of terminally blocked alanine di- and tri-peptides. J.Mol.Struct. 291, 271-286 (1993).

96.  Koca J., Carlsen P.H.J.: DAISY, A Computational Method. A Novel Tool for a Study of Conformational Behavior of Flexible Molecules. J.Mol.Struct. (Theochem) 257, 105-130 (1992).

97.  Koca J., Carlsen P.H.J.: ROSE, a Computer Program for Automatic Generation of Probable Conformations. J.Mol.Struct. (Theochem) 257, 131-141 (1992).

98.  Koca J.: A Mathematical Model of Logical Structure of Chemistry. A Bridge between Theoretical and Experimental Chemistry and A General Tool for Computer Assisted Molecular Design. I. An Abstract Model. Theor. Chim. Acta 80, 29-50 (1991).

99.  Koca J.: A Mathematical Model of Logical Structure of Chemistry. A Bridge between Theoretical and Experimental Chemistry and A General Tool for Computer Assisted Molecular Design. II. Conformational and Reaction Changes. Theor. Chim. Acta 80, 51-62 (1991).

100.                  Koca J., Kratochvil M., Kvasnicka V., Matyska L., Pospichal J.: Synthon Model of Organic Chemistry and Synthesis Design, pp. 1-207. Lecture Notes in Chemistry 51. Springer-Verlag, Heidelberg 1989.

101.                  Matyska L., Koca J.: MAPOS: A Computer Program for Organic Synthesis Design Based on Synthon Model of Organic Chemistry J.Chem.Inf.Comp.Sci. 31, 380-386 (1991).

102.                  Koca J.: A Mathematical Model of Realistic Constitutional Chemistry. A Synthon Approach. I. An Algebraic Model of A Synthon. J.Math.Chem. 3, 73-90 (1989).

103.                  Koca J.: A Mathematical Model of Realistic Constitutional Chemistry. A Synthon Approach. II. The Model and Organic Synthesis. J.Math.Chem. 3, 91-115 (1989).

  1. Koca J.:  A Mathematical Model of The Synthon . Coll. Czech. Chem. Commun.  53, 1007-1017 (1988).
  2. Koca J.:  A Graph Model of The Synthon . Coll. Czech. Chem. Commun.  53, 3108-3118 (1988).
  3. Koca J.:  The Reaction Distance. Coll. Czech. Chem. Commun.  53, 3119-3130 (1988).
  4. Koca J., Kratochvíl M., Matyska L., Kvasnicka V.: Mathematical Model of Reorganization of Valence Electrons Involving Two Atoms . Coll. Czech. Chem. Commun.  51, 2637-2655 (1986).
  5. Balaz V.,  Koca J., Kvasnicka V., Sekanina M.:  A Metric for Graphs.  Cas. Pest. Matem.  111, 431-433 (1986).
  6.  Koca J., Kratochvíl M., Kvasnicka V.:  Reaction Mechanism Graphs . Coll. Czech. Chem. Commun. 50, 1433-1449 (1985).
  7.  Kratochvíl M.,  Koca J., Kvasnicka M.:  Logical structure of chemistry and its mathematical model IV. Schemes of Valence Electrons Redistribution in Course of Chemical Reactions.  Chem. Listy   79, 807-839 (1985). 
  8. Koca J., Novotný I., Simek M., Vrchlabsky M.:  Structure and Formation of Chemical Databasis for the Tutorial Computer Systems. Chem. Listy  78, 978-989 (1984) (in Czech).
  9.  Koca J., Kratochvíl M., Kunz M., Kvasnicka V.:  Valence States of Atoms and Their      Conversions . Coll. Czech Chem. Commun.  49, 1247-1261 (1984).
  10.  Kratochvíl M.,  Koca J., Kvasnicka M.:  Logical structure of chemistry and its mathematical model III. An Invective method for Modelling of Chemical Reactions. Chem. Listy  78, 1-34 (1984).
  11.  Kvasnicka M., Kratochvíl M.,  Koca J.:  Reaction Graphs . Coll. Czech Chem. Commun.  48, 2284-2304 (1983).
  12. Koca J., Novotný I., Simek M., Vrchlabský M.:  Chemistry Instruction with an Aid of Computer.  Chem. Listy  77, 60-73 (1983) (in Czech).


Current Co-workers, Collaborators and Students:


Dr. Zdenek Kriz (1991-)

Dr. Petr Kulhanek (1999-)

Dr. Martin Prokop (1996-)

Dr. Radka Svobodova Varekova (1998-)

Dr. Stano Kozmon (2008-)

Doc. Dr. Michaela Wimmerova (1995-1998, 2001-)

Prof. Dr. Jiri Sponer (1999-)



Prof. Dr. Per H.J. Carlsen (NTNU, Norway, 1989-)

Dr. Anne Imberty (CERMAV, Grenoble, France, 1993-) 

Dr. Serge Perez  (CERMAV, Grenoble, France, 1993-) 

Prof. Dr. Robert Rittenhouse (Walla-Walla College, WA, USA, 1999-)

Prof. Dr. Chang-Guo Zhan (University of Kentucky, Lexington, KY, USA, 1999-)

Dr. Haluk Resat (Pacific Northwest National Lab, WA, USA, 1999-)


Michal Otyepka (Palacky University, Olomouc, Ph.D. with prof. Lasovsky, 2005)


Kamila Reblova (Ph.D., 2005)

Nikola Kostlanova (Ph.D., 2006)

Martina Budova (PhD, 2006)

Jan Adam ((Ph.D., 2010)

Jiri Wiesner (Ph.D., 2011)

Zuzana Novotna Jirouskova (Ph.D., 2011)

Jan Alan (Ph.D., 2011)

Jiri Fukal (Ph.D., 2011)

Jakub Stepan (Ph.D., 2013)

Zora Strelcova (Ph.D., 2013)

Crina Maria Ionescu (Ph.D., 2013)

Josef Pasulka (Ph.D., 2013)

Sushil Kumar Mishra (Ph.D., 2013)




Past Co-workers, Collaborators and Students:



Navnit Kumar Mishra (Ph.D., 2009)

Dr. Eva Fadrna (1992-2009)

Doc. Dr. Jiri Damborsky (1993-2008)

Ales Kosina (Ph.D.,  --)

Martin Petrek (Ph.D., --)

Jiri Matousek (Ph.D., --)

Iveta Bartova (Ph.D., 2006)

Lenka Snajdrova (PhD., 2006)

Filip Razga (PhD., 2006)

Michal Bohac (Ph.D.,2005)

Jan Kmunicek (Ph.D., 2004)

Lubos Vrbka (M.S.,2003)

Sari Ylitepsa (M.S., 2003)

Dr. Michal Cajan (Ph.D., 2002)

Dr. Richard Stefl (Ph.D., 2002)

Klara Hladeckova (M.S., 2001)

Zdenek Vytiska (M.S., 2001)

Sofiane Kettou (M.S., 2001)

Dr. Pavla Petrova-Sitkova (Ph.D., 2000)

Martin Ludin (M.S.,1999)

Jiri Pridal (B.A.,1999)

Dr. Michal Kuty (Ph.D.,1999)

Dr. Martin Cernohorsky (Ph.D.,1998)

Dr. Jan Gruza (Ph.D.,1998)

Dr. Lukas Trantirek (M.S.,1998)

Lukas Garcic (M.S.,1998)

Jakub Fabian (M.S.,1998)

Miloslava Benesova (M.S.,1998)

Tomas Cerny (M.S.,1997)

Jiri Benes (M.S.,1996)

Pavel Novak (M.S.,1996)

Dr. Jiri Czernek (M.S.,1995)

Iveta Bartosova (M.S.,1995)

Zbynek Hader (M.S.,1995)

Iva Kleinova (M.S.,1992)

Jana Plevova (M.S.,1990)

Vera Sobotkova (M.S.,1988)

Marie Hrabalova (M.S.,1986)

Last modification: Thu Sep 9 12:00:00 MET 2010